Prenylflavonoids and prenyl/alkyl-phloroacetophenones: synthesis and antitumour biological evaluation

Several prenylflavonoids have been synthesised and tested against human tumour cell lines. The prenyl unit has been geranyl or a labdane diterpene. These labdane-flavonoids have been synthesised for the first time. The antitumour activity increase with the prenylation at C-8 position. Twenty-three C and O-prenylated acylphloroglucinols have been synthesised as well. In this case the C-alkylation products have resulted, in general, more active.

Differences in delta13C and delta15N stable isotopes in the pearly razorfish Xyrichtys novacula related to the sex, location and spawning period

In the present study, Xyrichtys novacula (Labridae) were sampled at five locations around the islands of Ibiza and Formentera (western Mediterranean Sea). Isotopic signatures of delta13C, delta15N and the C:N ratio were analysed in relation to locality, sex and size differences. delta13C and delta15N partitioning was also studied in the reproductive spawning period. There were significant differences in the delta13C signature between localities for both sexes, but not for delta15N. Sex differences were also found with a mean +/-s.e. value of -17.38 +/- 0.06 per thousand delta13C and 8.36 +/- 0.05 per thousand delta(15)N for females and -17.17 +/- 0.07 per thousand delta13C and 8.80 +/- 0.06 per thousand delta15N for males. Increasing total length in both sexes was positively correlated with delta15N enrichment and a significant positive linear regression was established for both variables. During the reproductive spawning period, there were changes in delta13C fractioning with enrichment in postspawning females and males (with respect to prespawning and spawning periods) and delta(15)N impoverishment in postspawning females (with respect to prespawning and spawning periods). Xyrichtys novacula uses local food sources, as confirmed by delta(13)C and delta(15)N, and females and males use different food sources, thus avoiding intraspecific competition. This was confirmed by delta15N enrichment as size increased. Spawning leads to special requirements for gonad maturation, which is reflected in the isotopic signatures for both sexes.

Novel (60%) and recurrent (40%) androgen receptor gene mutations in a series of 59 patients with a 46,XY disorder of sex development

BACKGROUND

Androgen receptor (AR) gene mutations are the most frequent cause of 46,XY disorders of sex development (DSD) and are associated with a variety of phenotypes, ranging from phenotypic women [complete androgen insensitivity syndrome (CAIS)] to milder degrees of undervirilization (partial form or PAIS) or men with only infertility (mild form or MAIS).

OBJECTIVE

The aim of the study was to characterize the contribution of the AR gene to the molecular cause of 46,XY DSD in a series of Spanish patients.

SETTING

We studied a series of 133 index patients with 46,XY DSD in whom gonads were differentiated as testes, with phenotypes including varying degrees of undervirilization, and in whom the AR gene was the first candidate for a molecular analysis.

METHODS

The AR gene was sequenced (exons 1 to 8 with intronic flanking regions) in all patients and in family members of 61% of AR-mutated gene patients.

RESULTS

AR gene mutations were found in 59 individuals (44.4% of index patients), of whom 46 (78%) were CAIS and 13 (22%) PAIS. Fifty-seven different mutations were found: 21.0% located in exon 1, 15.8% in exons 2 and 3, 57.9% in exons 4-8, and 5.3% intronic. Twenty-three mutations (40.4%) had been previously described and 34 (59.6%) were novel.

CONCLUSIONS

AR gene mutation is the most frequent cause of 46,XY DSD, with a clearly higher frequency in the complete phenotype. Mutations spread along the whole coding sequence, including exon 1. This series shows that 60% of mutations detected during the period 2002-2009 were novel.

Replacement of fresh water use by final effluent recovery in a highly optimized 100% recovered paper mill

A further closure of the water circuit in paper mills with a relative high optimization of their water network is limited by the increase of contamination in the water and runnability problems of the paper machine. Therefore, new strategies for saving water must be focussed on the treatment of final effluents of the paper mill, aiming to obtain high quality water that may replace fresh water use in some applications. An appropriate treatment train performed at pilot scale, consisting on a previous clarification stage followed by anaerobic and aerobic treatments, ultrafiltration, and reverse osmosis, made possible producing the highest water quality from the final effluent of the mill. Anaerobic pre-treatment showed very good performance assisting the aerobic stage on removing organics and sulphates, besides it produced enough biogas for being considered as cost-effective. Permeate recovery depended on the silica content of the paper mill effluent, and it was limited to a 50-60%. The reject of the membranes fully met the legislation requirements imposed to effluents arriving to municipal wastewater treatment plants.

A CFSE-based assay of proliferative response of lymphocytes to stimulation with dengue viruses

Dengue viruses (DENVs) are human pathogens that constitute a significant threat worldwide. Since they up-regulate MHC class I molecules; the cell-mediated immunity may play an important role in the defense against viruses. In this work, we tested a CFSE-based assay in determining proliferative response of lymphocytes isolated from mice or monkeys previously immunized with various DENV antigens to in vitro stimulation with DENVs. A positive proliferative response was obtained with lymphocytes of animals immunized with either live DENV-2 or its recombinant proteins. A similar result was also obtained with CD8+ T cells from mice immunized with live DENV-1 or DENV-2 following stimulation with homologous viruses. A comparison of the carboxyfluorescein diacetate succinimidyl ester (CFSE)-based and a 3H-thymidine incorporation-based assays of proliferative response of total lymphocytes showed a fair correlation of results of both assays. However, the CSFE-based assay offers in addition the determination of contribution of the CD8+ or other subsets of T cells to total proliferative response. These results represent the first and successful application of a CFSE-based assay to the evaluation of cell-mediated immunity to DENVs. This assay might be also exploited in testing candidate DENV vaccines.

Deep subthreshold Xi;{-} production in Ar + KCl reactions at 1.76A GeV

We report first results on a deep subthreshold production of the doubly strange hyperon Xi;{-} in a heavy-ion reaction. At a beam energy of 1.76A GeV the reaction Ar + KCl was studied with the High Acceptance Di-Electron Spectrometer at SIS18/GSI. A high-statistics and high-purity Lambda sample was collected, allowing for the investigation of the decay channel Xi;{-} --> Lambdapi;{-}. The deduced Xi;{-}/(Lambda + Sigma;{0}) production ratio of (5.6 +/- 1.2_{-1.7};{+1.8}) x 10;{-3} is significantly larger than available model predictions.

Automated identification of diagnosis and co-morbidity in clinical records

OBJECTIVES

Automated understanding of clinical records is a challenging task involving various legal and technical difficulties. Clinical free text is inherently redundant, unstructured, and full of acronyms, abbreviations and domain-specific language which make it challenging to mine automatically. There is much effort in the field focused on creating specialized ontology, lexicons and heuristics based on expert knowledge of the domain. However, ad-hoc solutions poorly generalize across diseases or diagnoses. This paper presents a successful approach for a rapid prototyping of a diagnosis classifier based on a popular computational linguistics platform.

METHODS

The corpus consists of several hundred of full length discharge summaries provided by Partners Healthcare. The goal is to identify a diagnosis and assign co-morbidi-ty. Our approach is based on the rapid implementation of a logistic regression classifier using an existing toolkit: LingPipe (http://alias-i.com/lingpipe). We implement and compare three different classifiers. The baseline approach uses character 5-grams as features. The second approach uses a bag-of-words representation enriched with a small additional set of features. The third approach reduces a feature set to the most informative features according to the information content.

RESULTS

The proposed systems achieve high performance (average F-micro 0.92) for the task. We discuss the relative merit of the three classifiers. Supplementary material with detailed results is available at: http:// decsai.ugr.es/~ccano/LR/supplementary_ material/

CONCLUSIONS

We show that our methodology for rapid prototyping of a domain-unaware system is effective for building an accurate classifier for clinical records.

Muscle and scale isotopic offset of three fish species in the Mediterranean Sea: Dentex dentex, Argyrosomus regius and Xyrichtys novacula

Diet information of organisms was traditionally acquired by the use of lethal techniques (gut content or muscle delta(13)C and delta(15)N isotopic ratios). An increase in the number of isotopic ratio studies and the vulnerability of some species have led to increased use of non-lethal methodologies for conservation purposes. In the present work we have compared the delta(13)C and delta(15)N isotopic signals of muscle and scales of three different fish species in order to test fish-scale sampling as a non-lethal technique in fish trophodynamics. A positive correlation was found between muscle and scales in Argyrosomus regius and Xyrichtys novacula, while Dentex dentex showed no correlation due to the small length range of this species. The isotopic offset (Delta(13)C and Delta(15)N) between muscle and scales was significantly different among species (analysis of variance (ANOVA), p < 0.001) with Tukey's post-hoc HSD indicating a tissue offset difference (p < 0.001) for both stable isotopes in all species, except for Delta(13)C between A. regius and X. novacula and for Delta(15)N between D. dentex and X. novacula (p > 0.05). Mean delta(13)C and delta(15)N values between species showed significant differences (paired t-test, p < 0.01) between muscle and scale with an enrichment for delta(13)C and a depletion for delta(15)N. Spatial differences were found in the Delta(13)C of X. novacula between the studied locations, while no differences were found for Delta(15)N, indicating that non-geographical differences should be considered in the application of scales instead of muscle for (15)N, while for (13)C differences in the geographical isotopic offset should be considered.

Post-surgical enterococcal meningitis: Clinical and epidemiological study of 20 cases

Enterococcal post-surgical meningitis is an uncommon disease. 20 episodes of nosocomial post-surgical enterococcal meningitis diagnosed between 1994 and 2003 were retrospectively studied. During the period of study 20 cases of post-surgical enterococcal meningitis (60% female, mean age 55+/-18 y, range 16-78 y) were reviewed. The mean time between admission at the hospital and surgery was 26 (SD = 15) d (range 7-61 d). The most frequent underlying diseases were: intracerebral haemorrhage (55%), brain neoplasms (25%), head trauma (15%) and hydrocephalus (5%). 11 patients had previously received antibiotic treatment. The isolates identified were Enterococcus faecalis (n = 18) (90%), E. faecium (1) and E. durans (1). 11 patients had polymicrobial infections. The treatment most frequently used was vancomycin alone or with other antibiotics (11). In 5 patients intrathecal vancomycin (20 mg/d) was also added. The mortality rate was not different in intrathecally treated patients. Cerebrospinal fluid (CSF) devices were removed in 8 patients. Four patients died due to the infection. Mortality was significantly associated with lack of removal of the CSF devices (p = 0.04). Enterococcal spp. are a cause of nosocomial meningitis associated with neurosurgical procedures and the presence of neurological devices.

Quantitative study of Leydig cell populations in mice exposed to low doses of cadmium

Leydig cell morphological changes were evaluated using morphometric and stereological methods in male mice exposed to low doses of cadmium. A possible reversibility of the changes after cadmium withdrawal was also considered. Nuclear morphological parameters and stereological densities of the Leydig cell population were lower in the cadmium-exposed groups than in the control. The withdrawal of cadmium did not lead to any significant recovery of the morphological parameters. Nevertheless, numerical density increased significantly in the withdrawn groups, suggesting that the hyperplasia of interstitial cells could try to relieve morphological damage after cadmium withdrawal.

Microarray study of gene expression profiles in peripheral blood samples from lung cancer patients before and after erlotinib treatment

e19072

Background: The gene expression profile in peripheral blood samples from lung cancer patients is a potential predictor to treatment response. Methods: The study has been developed using 10 healthy volunteers as the control group and 10 lung cancer patients (stage IV). Written informed consent was obtained being the protocol approved by the local Clinical Research and Ethics Committee. Peripheral blood samples were obtained from lung cancer patients before (T0) and after treatment (T15d). RNA from peripheral blood samples was extracted and purified selecting 28S/18S ratios>1.5 to obtain cDNA and cRNA for hybridization of the 20,000 genes included in Human 20K CodeLink. An array from each participant was obtained in duplicate. For each array, 2 μg of cRNA was compared to 2 μg of healthy cRNA.. Significant genes were found using Significance Analysis of Microarrays which uses repeated permutations of the data. Results: The selected genes were expressed >3-fold with a false discovery rate =0.05. Before treatment (T0) when patients were compared to healthy volunteers there was an increase in the expression of: histone 1 H4c, transforming growth factor beta 2, endothelial cell growth factor 1 (platelet-derived), glucose-6-phosphatase catalytic 2, Relaxin 3 receptor 1, Insulin-like growth factor binding protein 2, RAS-like family 11 member B, and ELK4. After treatment (T15d), when each lung cancer patient's results were compared to their own before treatment results (T0), there was an increase in the expression of: Bcl2, myosin light polypeptide 4; interferon alpha-inducible protein 27; interferon gamma receptor 1; RASSF5, ARHGEF6, IGFBP5, tumor protein p53 inducible nuclear protein 1, peroxisome proliferative activated receptor gamma. Conclusions: The data presented identifies biologically relevant over-expressed genes in lung cancer. A validation of these results and the analysis of the genes that identify patients who will respond positively to erlotinib treatment is being carried out.

No significant financial relationships to disclose.

[Validity of a telephone survey for determining the prevalence of atopic dermatitis and its seasonal variation in Spain]

BACKGROUND

Atopic dermatitis is a eczematous disease of the skin with onset during childhood and subsequent flares. The UK Working Party (UKWP) defined the diagnostic criteria normally used for atopic dermatitis. The objective of this study was to assess the prevalence of atopic dermatitis according to these criteria.

METHODS

This was a 2-phase cross-sectional, epidemiologic computer-assisted telephone survey. Parents of children aged 14 years or less participated in the first phase to determine the prevalence of atopic dermatitis in Spain. In the second phase, 6 months later, parents of children with diagnosis of atopic dermatitis according to the UKWP diagnostic criteria in phase 1 were interviewed to assess seasonal variations in disease activity between the 2 phases.

RESULTS

In total, 1979 parents participated; 8.6 % of the children (95 % confidence interval, 7.4 %-9.8 %) were diagnosed with atopic dermatitis by telephone. Of these, 49.2 % had a family history of atopy and 41.3 % had been diagnosed with atopic dermatitis by a physician. Diagnosis by the physician and that made by interview agreed in 75.3 % of these cases. Of the factors associated with atopic dermatitis, it was found that increased body temperature, periods of stress, dust, use of/contact with wool or fiber clothes, and use of certain soaps and hygiene products showed seasonal variations.

CONCLUSIONS

The estimated prevalence of atopic dermatitis in children between 0 and 14 years old in Spain was 8.6 %. Certain factors associated with disease flares showed seasonal variations.

Global DNA methylation: a common early event in oral cancer cases with exposure to environmental carcinogens or viral agents

INTRODUCTION

Two separate molecular pathways have been proposed for the early carcinogenic events observed in the oral cavity and pharynx: one is associated with chemical etiological factors such as smoking and drinking, and the other one is associated with HPV insertion.

OBJECTIVE

A proof-of-principle study was performed to ascertain if global DNA methylation could be used to distinguish between the early molecular changes in premalignant oral lesions.

METHODS

Personal histories of tobacco and alcohol use were obtained by questionnaire. HPV insertion in tumor tissue was detected by polymerase chain reaction (PCR). Global DNA methylation levels were obtained using HPLC for fraction separation and mass spectrometry for quantification. Predictive simulations were performed to explore potential associations between different etiological factors and the global DNA methylation index. Significance of results was ascertained using Pearson's Chi-squared test.

RESULTS

The global methylation index was found to be 4.28 (95% CI, 4.1, 4.4) in an oral cancer case series. Pearson's chi squared test showed no statistically significant difference between cases that had smoking (p = 0.21), drinking (p = 0.31) or HPV insertion (p = 0.34) as etiologic risk factors, when compared to cases that did not. An inverse significant association between smoking and DNA methylation was observed. As the smoking effect increases, the global methylation index decreases, In addition, no associations between the probability of DNA methylation and drinking, or DNA methylation and HPV insertion were observed in simulations.

CONCLUSIONS

The global DNA methylation index was shown to vary for oral cancer cases with different etiologies. Smoking was inversely correlated with DNA methylation levels when generalized linear model simulations were performed. Future studies should look at global DNA methylation alterations associated to the progression from normal to premalignant oral epithelium tissue in a cohort of smokers and nonsmokers.

Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat

The availability of genetic maps and phenotypic data of segregating populations allows to localize and map agronomically important genes, and to identify closely associated molecular markers to be used in marker-assisted selection and positional cloning. The objective of the present work was to develop a durum wheat intervarietal genetic and physical map based on genomic microsatellite or genomic simple sequence repeats (gSSR) markers and expressed sequence tag (EST)-derived microsatellite (EST-SSR) markers. A set of 122 new EST-SSR loci amplified by 100 primer pairs was genetically mapped on the wheat A and B genome chromosomes. The whole map also comprises 149 gSSR markers amplified by 120 primer pairs used as anchor chromosome loci, two morphological markers (Black colour, Bla1, and spike glaucousness, Ws) and two seed storage protein loci (Gli-A2 and Gli-B2). The majority of SSR markers tested (182) was chromosome-specific. Out of 275 loci 241 loci assembled in 25 linkage groups assigned to the chromosomes of the A and B genome and 34 remained unlinked. A higher percentage of markers (54.4%), localized on the B genome chromosomes, in comparison to 45.6% distributed on the A genome. The whole map covered 1,605 cM. The B genome accounted for 852.2 cM of genetic distance; the A genome basic map spanned 753.1 cM with a minimum length of 46.6 cM for chromosome 5A and a maximum of 156.2 cM for chromosome 3A and an average value of 114.5 cM. The primer sets that amplified two or more loci mapped to homoeologous as well as to non-homoeologous sites. Out of 241 genetically mapped loci 213 (88.4%) were physically mapped by using the nulli-tetrasomic, ditelosomic and a stock of 58 deletion lines dividing the A and B genome chromosomes in 94 bins. No discrepancies concerning marker order were observed but the cytogenetic maps revealed in some cases small genetic distance covered large physical regions. Putative function for mapped SSRs were assigned by searching against GenBank nonredundant database using TBLASTX algorithms.

Collaborative text-annotation resource for disease-centered relation extraction from biomedical text

Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature. Relation extraction systems cannot be developed without substantial datasets annotated with ground truth for benchmarking and training. The creation of such datasets is hampered by the absence of a resource for launching a distributed annotation effort, as well as by the lack of a standardized annotation schema. We have developed an annotation schema and an annotation tool which can be widely adopted so that the resulting annotated corpora from a multitude of disease studies could be assembled into a unified benchmark dataset. The contribution of this paper is threefold. First, we provide an overview of available benchmark corpora and derive a simple annotation schema for specific binary relation extraction problems such as protein-protein and gene-disease relation extraction. Second, we present BioNotate: an open source annotation resource for the distributed creation of a large corpus. Third, we present and make available the results of a pilot annotation effort of the autism disease network.

Waste management from pulp and paper production in the European Union

Eleven million tonnes of waste are produced yearly by the European pulp and paper industry, of which 70% originates from the production of deinked recycled paper. Wastes are very diverse in composition and consist of rejects, different types of sludges and ashes in mills having on-site incineration treatment. The production of pulp and paper from virgin pulp generates less waste but the waste has similar properties to waste from the production of deinked pulp, although with less inorganics. Due to legislation and increased taxes, landfills are quickly being eliminated as a final destination for wastes in Europe, and incineration with energy recovery is becoming the main waste recovery method. Other options such as pyrolysis, gasification, land spreading, composting and reuse as building material are being applied, although research is still needed for optimization of the processes. Due to the large volumes of waste generated, the high moisture content of the waste and the changing waste composition as a result of process conditions, recovery methods are usually expensive and their environmental impact is still uncertain. For this reason, it is necessary to continue research on different applications of wastes, while taking into account the environmental and economic factors of these waste treatments.

Endogenous lipid pneumonia in rats after subacute exposure to CdCl2

The objective of this report was to study lung cellular lesions in Wistar rats after subacute oral exposition to CdCl2. The experimental groups were exposed to CdCl2, through their drinking water in a concentration of 1 g/L, continuously for a period of 9 days. Histologically, all the exposed animals showed the incidence of interstitial pneumonia; hyperplasia of type II pneumocytes and Clara cells; the presence of foamy macrophages; and lesions linked to the existence of endogenous lipid pneumonia. Endogenous lipid pneumonia after CdCl2 exposure has not been previously described; and in its pathogenesis, hyperplasia of type II pneumocytes and Clara cells activation could play an important role.